The Apolobamba area in the Andean Plateau has extensive grasslands that support threatened species such as vicuna (Vicugna vicugna). Knowledge of the organic matter dynamics is fundamental to the understanding of the impacts of animal grazing on the C reservoirs and soil fertility that are essential to the maintenance of biodiversity in high altitude grasslands. The objective of this research was to understand the impacts of animal grazing on soil organic matter stabilization and mineralization in high altitude grasslands. Soil samples were collected from 8 representative zones of population densities of vicuna in the Apolobamba area. High amount of total organic C stock (5.2 kg m− 2), recalcitrant C contents (3.7 kg m− 2) and recalcitrance index (0.8) highlight the importance of these high altitude grasslands as stable C reservoirs. We found higher C–CO2 releases at 25 °C (2786.9 ± 343.1 g CO2 m− 2 yr− 1) than at 15 °C (70.2 ± 3.1 g CO2 m− 2 yr− 1). A negative influence of domestic camelid grazing on the decreasing of soil organic C stocks was observed. Therefore, there is an urgent need to establish soil protection strategies to keep the soil C reservoirs and to preserve the biodiversity and sustainable management of the vicuna in the Bolivian Andean grasslands.